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PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update.

Xiaowei Wang1, Athanasia Spandidos, Huajun Wang

  • 1Department of Radiation Oncology, Washington University School of Medicine, 4511 Forest Park Ave, Saint Louis, MO 63108, USA.

Nucleic Acids Research
|November 17, 2011
PubMed
Summary

PrimerBank now offers over 497,000 validated primer pairs for human and mouse genes, facilitating efficient polymerase chain reaction (PCR) and quantitative PCR (qPCR) experiments. This resource simplifies gene expression analysis with uniform amplification conditions.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Designing optimal primer sequences for polymerase chain reaction (PCR) and quantitative PCR (qPCR) is a significant experimental hurdle.
  • Existing resources may lack comprehensive coverage or experimental validation for primer pairs.
  • Quantitative PCR (qPCR) is increasingly used to validate findings from high-throughput gene expression studies like microarrays and RNA-Seq.

Purpose of the Study:

  • To describe a major update to PrimerBank, a comprehensive resource for validated PCR and qPCR primers.
  • To expand the primer coverage for human and mouse genes using an updated design algorithm.
  • To provide primers suitable for uniform, high-throughput, and allele-invariant amplification conditions.

Main Methods:

  • An updated primer design algorithm, based on previous approaches, was employed using current genomic data from NCBI.
  • New primers were designed to cover 17,076 human genes and 18,086 mouse genes.
  • Experimental validation of primer pairs was a key feature of the PrimerBank resource.

Main Results:

  • The updated PrimerBank contains 497,156 primers, a 62% increase from the previous version.
  • These primers cover 36,928 human and mouse genes, representing approximately 94% of known protein-coding sequences.
  • PrimerBank primers are validated for stringent and allele-invariant amplification, ensuring reliable PCR and qPCR performance.

Conclusions:

  • PrimerBank provides a significantly expanded and experimentally validated collection of primers for human and mouse genes.
  • The resource supports high-throughput and genome-wide quantitative PCR (qPCR) applications with uniform reaction conditions.
  • PrimerBank facilitates more accurate and sensitive gene expression analysis, aiding in the reanalysis of data from exploratory technologies.